User: zhaoliang0302

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Posts by zhaoliang0302

<prev • 16 results • page 1 of 2 • next >
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Comment: C: GISTIC segment overlap error
... Thanks, but I filtered Primary Solid Tumor samples and it still shows error after GISTIC. I find out 22-25 chars of Tumor-Sample-Barcode can also differ in the same patient. It will result in error. Can you help me? ...
written 11 months ago by zhaoliang03020
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Comment: C: How to remove outliers using PCA in R?
... Thanks, I save this plot as PDF file (large size) and then zoom in to get the outlier samples. It sounds silly but it really works :-) ...
written 12 months ago by zhaoliang03020
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Comment: C: How to remove outliers using PCA in R?
... Yes, all tumor samples are from the same dataset. The clinical data doesn't contains batch information. So I want to remove these samples directly. ...
written 12 months ago by zhaoliang03020
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Comment: C: How to remove outliers using PCA in R?
... I downloaded this RNAseq data and just explore it. Considering the large samples, I think remove these 'outlier' samples is not a risk. ...
written 12 months ago by zhaoliang03020
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Comment: C: How to remove outliers using PCA in R?
... The data is a dataframe of RNAseq FPKM expression file, rows correspond to genes and columns to samples. library("FactoMineR") library("factoextra") pca_data <- as.data.frame(t(RNAseq_data)) pca_data$group <- c(rep('GBM',100),rep('rGBM',100)) pca <- PCA(pca_data[,1:(nc ...
written 12 months ago by zhaoliang03020
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How to remove outliers using PCA in R?
... Hi, I detected several outliers among my samples by plotting PCA. But I don't know how to remove this samples![PCA plot][1] The outlier samples is marked by the red circle. Thanks [1]: https://i.loli.net/2019/07/23/5d36ccb13191139502.png ...
R pca written 12 months ago by zhaoliang03020
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Comment: C: How to do FPKM differential analysis?
... Hi, If I understand right, you mean I can merge two FPKM data from two batches without considering the batch effect? I have two batch rnaseq FPKM data now (counts not avaliable) and I want to merge them into a whole dataset. I know Deseq can deal with it by treat batch as variable for counts data. S ...
written 12 months ago by zhaoliang03020
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Comment: C: How to do FPKM differential analysis?
... Thanks a lot. It really helps☺ ...
written 12 months ago by zhaoliang03020
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How to do FPKM differential analysis?
... Hello, I want to do diffrential analysis on rnaseq **FPKM** data (can't get **count**). DEseq and edgR need raw count as input, so how should I do? Is it suitable for **limma** package? ...
fpkm deseq rna-seq limma written 12 months ago by zhaoliang03020 • updated 12 months ago by kristoffer.vittingseerup3.4k
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Comment: C: Should I pre-normalize RNAseq data before combat?
... Hello Kevin, Much thanks. I know what you said now. I plot PCA and found a signifiant difference between two batches. After your explanation, I won't use **combat** . Now the question is I don't know the expression data is **count** or **FPKM**, the official documentation is showed in the pictures ! ...
written 12 months ago by zhaoliang03020

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